Microscopy Thread

[EnterName]

Reef2Reef Microscopy Thread ​

Your tank is packed with life you might have never noticed: rotifers, protists, larval worms, sponges, micro algae, etc. Most of it is smaller than a grain of salt but still absolutely fascinating. This thread is where the Reef2Reef community can take a closer look at what lives "hidden" in our tanks.

Using DIC microscopy, a technique that turns transparent, near-invisible critters into glowing 3D sculptures of light and shadow, I'll be posting high-res images and videos of whatever's crawling, swimming, or drifting through our reef tanks. Everyone is invited to share their microscopy images/videos as well!

No Microscope? No problem. You don't need one to enjoy this thread nor to pursue the hobby. It can be a lot of fun though and help with the proper identification of what you are dealing with.

I hope you enjoy the first few images I have taken for this thread:

1. Amphiprion ocellaris (Common Clownfish) eggs.

(Clownfish egg - Day 1)

(Clownfish egg - Day 5)
It is astonishing how much changes within a few days.​

2. Coral samples

(Briareum sp. polyp with dense zooxanthellae population)
These little orange circles are Symbiodinium sp. (dinoflagellates) living in symbiosis with their host coral to provide energy via photosynthesis in exchange for anorganic molecules and a safe place to stay. Most of you may know them as "zooxanthellae".

(Rhodactis sp. "Rhodactis Plutonium" cnidocytes and some zooxanthellae)
Ever wondered how corals defend themselves? These bean shaped cells are everywhere on corals and will literally shoot a toxin-loaded string (cnidocyst, well visible on the image) into whatever activates them.

(Briareum sp. "sclerite")
Even though Briareum spp. are considered a soft coral they still grow these calcitic spicules that act as a skeleton. These are mainly found in the tissue that is growing on the rocks and holds the polyps in place.
​

3. Various critters

(Some Ostracod I found in the stomach of a flatworm)
Armored crusaceans that you can find sifting through detritus in the substrate. They can look a bit creepy when moving around, but they are beneficial and harmless.

(Juvenile Flatworm. This specimen should be an "Acoel Flatworm". They can be distinguished from "Ghost Flatworms" by their darker coloration caused by their Zooxanthellae. See post #85)
There are thousands of different flatworm species, most of them aren't welcome in a reef tank, but these ones are "ok". Their population can explode and they eat copepods, but at least they don't harm corals, fish, or inverts. This specimen was maybe 1mm in length, but they can grow up to like 4mm.
​

4. Algae and Protists

(Dinoflagellate, probably Ostreopsis sp.)
One of the more dangerous dinoflagellates due to its toxicity, but finding a few single cells from time to time is absolutely normal and nothing to worry about. I had quite a lot of them for some time, but the toxin never really became an issue. My copperband butterflyfish even ate a lot of them every time I scraped the glass clean. I frequently found them together with diatoms.

(Dinoflagellate, probably Prorocentrum sp., maybe P. lima?)
Another dinoflagellate species I had a lot of for some time. Their numbers grew proportional to the diatom population which might suggest they are preying on diatoms or simply thrive in the same environments.

(Diatom, possibly Licmophora sp.)
These little guys are very abundant in my tank. They attach to pretty much every surface they can find and make up a major portion of the stuff that needs to be scraped off of my tank glass.


Equipment​

Most images are taken with my Leica/Leitz DMRB microscope using DIC microscopy and focus stacking (some are dark-field or simple bright-field microscopy images though). I'm currently using a Sony A7iii to take images in a magnification range from 50x to 1000x.

Table of Contents​

Posts (ordered by date):
[Photo+Video] Amphidinium sp. (Page 1, Post #3)
[Video] Polychaete (Page 1, Post #4)
[Video] Parenchymella larvae of a sponge (Page 1, Post #6)
[Photo] Bubble algae (Page 1, Post #8)
[Photo] Copepod nauplii (Page 1, Post #11)
[Video] Some unidentified "worm" (Page 1, Post #12)
[Photo+Video] Diatoms, likely Nitzschia sp. (Page 1, Post #16)
[Video] Sabellidae or Serpulidae tube-worm (Page 2, Post #24)
[Video] Unknown specimen & possibly tubeworm larvae (Page 2, Post #39)
[Video] Collection of short clips (Page 2, Post #40)
[Video] Unidentified, most likely Trachelocercid ciliate (Page 3, Post #46)
[Video] Spawning Rock Anemone + Gametes (Page 3, Post #50)
[Video] Hydroid Medusa (Page 3, Post #51)
[Video] Cyanobacterium (Spirulina sp.?) (Page 3, Post #52)
[Photo] Branched Halymenia (Halymenia durvillei) (Page 3, Post #60)
[Video] Digitate Hydroid (Page 4, Post #61)
[Photo] Ball Sponges (Tethya sp.?) (Page 4, Post #68)
[Photo] Sea lettuce (Ulva or Ulvaria sp.) (Page 4, Post #69)
[Photo+Video] Hydroid, possibly Obelia sp. (Page 4, Post #80)
[Photo+Video] Spirorbid worm (Page 5, Post #81)
[Photo+Video] Sponge, possibly Clathrina sp. (Page 5, Post #82)
[Photo+Video] Pineapple Sponge, Sycon sp. (Page 5, Post #83)
[Video] Unknown specimen (Page 5, Post #84)
[Photo+Video] Acoel Flatworm (Heterochaerus sp.?) (Page 5, Post #85)
[Photo] Unidentified diatoms (Page 5, Post #91)
[Photo+Video] Nematodes (Page 5, Post #92)
[Video] Trachelocercidae Ciliate? (Page 5, Post #93)
[Photo] Unidentified specimen (Page 5, Post #94)
[Video] Euplotida Cililate (Aspidisca sp.?) (Page 5, Post #100)
[Photo+Video] Cat Sea Slug (Vayssierea felis)? (Page 6, Post #101)
[Photo+Video] Tanaid? (Page 6, Post #102)
[Photo+Video] Zoospores (Page 6, Post #103)
[Photo+Video] Munnidae Isopod (Page 6, Post #106)
[Video] Euplotida Ciliate (Euplotes sp.?) (Page 7, Post #123)
[Video] Aiptasia/Exaiptasia (Page 7, Post #124)
[Video] Anthoathecata, possibly Capitata (Page 7, Post #125)
[Video] Unidentified Flatworm (Page 7, Post #127)




Posts (ordered by specimen):

Red & Green Algae
[Photo] Bubble algae (Page 1, Post #8)
[Photo] Branched Halymenia (Halymenia durvillei) (Page 3, Post #60)
[Photo] Sea lettuce (Ulva or Ulvaria sp.) (Page 4, Post #69)
[Photo+Video] Zoospores (Page 6, Post #103)

Bacteria
[Video] Cyanobacterium (Spirulina sp.?) (Page 3, Post #52)

Ciliates
[Video] Unidentified, most likely Trachelocercid ciliate (Page 3, Post #46)
[Video] Trachelocercidae Ciliate? (Page 5, Post #93)
[Video] Euplotida Ciliate (Page 5, Post #100)
[Video] Euplotida Ciliate (Euplotes sp.?) (Page 7, Post #123)

Corals
[Video] Spawning Rock Anemone + Gametes (Page 3, Post #50)
[Video] Aiptasia/Exaiptasia (Page 7, Post #124)

Crustaceans
[Photo] Copepod nauplii (Page 1, Post #11)
[Photo+Video] Tanaid? (Page 6, Post #102)
[Photo+Video] Munnidae Isopod (Page 6, Post #106)

Diatoms
[Photo] Licmophora sp. (Page 1, Post #1, this very post)
[Photo+Video] Diatoms, likely Nitzschia sp. (Page 1, Post #16)
[Photo] Unidentified diatoms (Page 5, Post #91)

Dinoflagellates & Protists
[Photo] Prorocentrum sp. & Ostreopsis sp. (Page 1, Post #1, this very post)
[Photo+Video] Amphidinium sp. (Page 1, Post #3)

Hydrozoa
[Video] Hydroid Medusa (Page 3, Post #51)
[Video] Digitate Hydroid (Page 4, Post #61)
[Photo+Video] Hydroid, possibly Obelia sp. (Page 4, Post #80)
[Video] Anthoathecata, possibly Capitata (Page 7, Post #125)

Sponges
[Video] Parenchymella larvae of a sponge (Page 1, Post #6)
[Photo] Ball Sponges (Tethya sp.?) (Page 4, Post #68)
[Photo+Video] Root-like growing sponge, possibly Clathrina sp. (Page 5, Post #82)
[Photo+Video] Pineapple Sponge, Sycon sp. (Page 5, Post #83)

Worms
[Video] Polychaete (Page 1, Post #4)
[Video] Some unidentified "worm" (Page 1, Post #12)
[Video] Sabellidae or Serpulidae tubeworm (Page 2, Post #24)
[Photo+Video] Spirorbid worm (Page 5, Post #81)
[Photo+Video] Acoel Flatworm (Heterochaerus sp.?) (Page 5, Post #85)
[Photo+Video] Nematodes (Page 5, Post #92)

Other
[Video] Unknown specimen & possibly tubeworm larvae (Page 2, Post #39)
[Video] Collection of short clips (Page 2, Post #40)
[Video] Unknown specimen (Page 5, Post #84)
[Photo] Unidentified specimen (Page 5, Post #94)
[Video] Cat Sea Slug (Vayssierea felis)? (Page 6, Post #101)

 

[Euphyllia97]

Copepod and a sample of green algae during my “uglies” phase. Would love to see some parasites on this topic :)

 

[EnterName]

Dinoflagellate
(Amphidinium spp.)​

Amphidinium are dinoflagellates that come in different shapes but nearly always have a distinctive feature at their top section which is often referred to as "beak" (or more scientifically "epicone"). This makes them easy to distinguish from the other common dinoflagellates in reef tanks.

(Amphidinium sp. with clearly visible epicone at the top)
​

Amphidinium species tend to stay in the substrate even at night which makes it difficult to manually remove them. However, the cell above has been found in damaged coral tissue among diatoms and cyanobacteria.

(Round Amphidinium sp.? in biofilm from my tank's back wall [1])​

Common Name	Dinos / Dinoflagellates / Amphidinium
Classification	Amphidinium sp.
Verdict	Harmful (in large numbers)
Size	≤ 60μm
Found	Substrate, Rockwork, Glass
Rarity	Obligatory (either rare or it takes over)

("Small cell" Amphidinium sp.)
​

It always bothered me that they are called dinoflagellates, but in contrast to other organisms it's really difficult to see their flagella in action. In the video below you can see the flagella quite well:

("Small cell" Amphidinium spp. between cyanobacteria)
​

[1]: Amphidinium is often described as assymmetric, but there are also circular/round individuals, where only the epicone is breaking the symmetry: https://www.researchgate.net/figure...i-AMJJ1-under-light-microscopy_fig5_327828744

 

[EnterName]

Polychaete
(Unknown sp.)

(Some polychaete recorded in dark-field)
​

Common Name	Bristle Worm
Classification	Polychaete (genus and species unknown)
Verdict	Depends on genus/species. In this case apparently harmless filter feeder
Size	Usually ≤ 5cm (2")
Found	Detritus samples, under rockwork
Rarity	Common

 

[nitrox2000]

The below images are thought to be an Amphidinium species of Dinoflagellates, although not the common variety usually found as it doesn't have a hook like mouth:

The below image is a more common Amphidinium, with a visible hook like mouth:

I have a attached a few videos below on the behaviour and swim patterns:

 

[EnterName]

Sponge larvae (Parenchymella larvae)
(Unknown sp.)

(Parenchymella larvae of some sponge annoying a little copepod)
​

Common Name	Sponge larvae
Classification	Phylum: Porifera (Unknown genus and species)
Verdict	Depends on genus/species
Size	50μm - 5mm (0.2")
Found	open water column
Rarity	Probably common, but hard to find

 

[Magok]

I smashed a bubble algae (seed bubble?) Between two slides

 

[EnterName]

Bubble Algae
(Boergesenia sp.? Derbesia sp. (Halycistis)?, Dictyosphaeria sp.? Valonia sp.? Ventricaria sp.?)​

I smashed a bubble algae (seed bubble?) Between two slides

I liked the idea so I decided to try the same at 400x magnification. The bubble itself has a weird "woven" texture (or messes with DIC microscopy) which I though was really fascinating.

(Squashed bubble)
​

Common Name	Bubble Algae
Classification	Boergesenia sp.? Derbesia sp. (Halycistis)?, Dictyosphaeria sp.? Valonia sp.? Ventricaria sp.?
Verdict	Nuisance
Size	≤ 5cm (2") per bubble
Found	Rockscape
Rarity	Common nuisance algae

(Chloroplasts, often with one or two pyrenoids visible as bubbles in the chloroplasts)
​

'm still searching on how to properly distinguish Valonia sp. from a Derbesia sp. gametophytes. As you may know, Derbesia is usually a green hair algae, but this is only its asexual form that reproduces by releasing so called "zoospores" or simply by breaking off filaments that grow wherever they settle. Derbesia has also a gametophyte form allowing it to release gametes to reproduce sexually. This form was once thought to be its own genus "Halicystis" and looks like bubble algae.

(In this image you can clearly see the actual "bubble wall" holding in chloroplasts)​

 

[Fish Fan]

Following

 

[BoaConservationist]

alot on my plate this weekend but I may have some contributions to this, will need to fully dive into it , thanks for the invite !

 

[EnterName]

Copepod nauplii
(Unknown sp.)

(Copepod nauplii)
​

I think there is room for improvement, but still a decent image for identification purposes if someone wonders what is "jumping" around under their microscope :)
These little guys are quite fast and it isn't too easy creating focus stack images of them.

(Another Copepod nauplii)
​

Common Name	Copepod nauplii
Classification	Class: Copepoda (genus/species unknown)
Verdict	Beneficial
Size	≤ 500μm
Found	Substrate, Detritus
Rarity	Common

 

[EnterName]

Unknown Specimen
(Polychaete larvae?)

I wasn't able to fully identify this little guy. It seems to be some annelid. It looks like a Polychaete larvae (or rather a Nectochaete), but the bristles (namely "chaetigers") seem to be missing.

Similar, but not equal in shape compared to the specimen in the other video. This could suggest they are larvae and still change their shape significantly. It could also mean we are looking at two different organisms.

​

Common Name	?
Classification	?
Verdict	?
Size	100μm - 150μm
Found	Detritus sample
Rarity	?

 

[MikeReefs]

Black Bug/Marine Mite on GHA. Not much is known about them but I’ve had them in a LPS tank and no corals were ever harmed. I believe they eat algea and detritus

 

[Hadla]

Love these! I’ve always wanted a decent microscope

 

[EnterName]

Love these! I’ve always wanted a decent microscope

Glad you like the images and videos :)

You don't need an expensive microscope to see/identify the things posted here. You can enjoy the micro-cosmos in your tank (or ponds, puddles, and more) with something between $50 and $200 just fine.

However, you will be limited to bright-field microscopy (background is white/bright and specimens appear flat). Dark-field is affordable, but will already cost a bit more (background is black/dark and specimens appear illuminated like for example the clownfish eggs). If you also want this 3D-Effect where specimens appear to cast a shadow (Differential Interference Contrast), it will get really expensive.

Just start cheap and see if this is something you want to keep doing.

 

[EnterName]

Diatoms
(Nitzschia sp.?)​

Diatoms are pretty much the first algae most reefers will come into contact with during the "ugly phase". It is commonly confused with dinoflagellates as the symptoms appear similar at first and both frequently appear together. However, diatoms are pretty harmless and easy to control with a bit of patience.

(Diatom bloom on newly introduced dry sand in reef tank)
​

Common Name	Diatoms
Classification	Nitzschia sp.?
Verdict	Neutral
Size	≤ 400μm
Found	Substrate, Glass
Rarity	Common (always present in every tank)

Diatoms form a "shell" (called "frustule") out of silicon dioxide [SiO₂] which they get from orthosilicic acid [Si(OH)₄] in the water. You can actually see this shell in the image above (the thin transparent "arms"). Many diatoms can move actively by pushing water through their frustule as you can see in the video below:

(Diatoms moving around and forming aggregates causing brown stains on the substrate)

(10x63 PL APO Immersion-Oil Objective Recording)​

They most often bloom in new tanks, but introducing new substrate or using insufficiently deionized RO/DI water for the ATO or during water changes can cause silicates to rise which often leads to a diatom bloom. The treatment is fairly easy: remove the silicate source and wait. Excessive silicates can also be removed with adsorber material if necessary.

(Probably Nitzschia sp. or maybe something like Cylindrotheca closterium?)​

 

[Dom]

1. Amphiprion ocellaris (Common Clownfish) eggs.

(Clownfish egg - Day 1)

(Clownfish egg - Day 5)
It is astonishing how much changes within a few days.

​

These Clownfish egg photos are fascinating. But the story is incomplete.

I would have enjoyed seeing the complete progression.

Thank you for sharing!

Dom

 

[EnterName]

These Clownfish egg photos are fascinating. But the story is incomplete.

I would have enjoyed seeing the complete progression.

Thank you for sharing!

Dom

That's a fair point, unfortunately I can't raise Clownfish babies right now and don't know if I can start another giant project :D

Would be really cool though, and I have been thinking about it a lot... Maybe some day :)

 

[TheMachinistReefer]

I've recently discovered how fascinating this side of the hobby is. I just have a cheap microscope, but it does the job!

 

[EnterName]

I've recently discovered how fascinating this side of the hobby is. I just have a cheap microscope, but it does the job!

Ostreopsis aside, I like the large diatoms. Is it a young tank or did you manage to maintain their population somehow? In my tank diatom diversity has declined over the years and I would really like to understand how to get some of these larger diatoms back.